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    	<title>Names on Nodes</title>
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		<meta name="Author" content="T. Michael Keesey" />
		<meta name="Description" content="Names on Nodes, a web application that performs the automatic application of biological nomenclature." />
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			<h1><span class="title">Names on Nodes</span></h1>
			<p class="subtitle">automated application of biological nomenclature</p>
			<h2>About <span class="title">Names on Nodes</span></h2>
			<p>
				<span class="title">Names on Nodes</span> is a web application that automatically applies biological nomenclature to datasets.
				Datasets may be uploaded as bioinformatics files (<span class="langname">Nexus</span>, etc.).
				<span class="title">Names on Nodes</span> uses the definitions of names to apply them to phylogenetic hypotheses.
			</p>
			<p>
				The basic principles which <span class="title">Names on Nodes</span> uses were laid out in:
			</p>
			<ul>
				<li>
					<span class="citation-authors">Keesey, T. M.</span> (2007 Sep 21).
					A mathematical approach to defining clade names, with potential applications to computer storage and processing.
					<span class="title">Zoologica Scripta</span>
					<span class="volume-number">36</span>(6):607&ndash;621.
					<a href="http://dx.doi.org/10.1111/j.1463-6409.2007.00302.x"><code>doi:10.1111/j.1463-6409.2007.00302.x</code></a>
				</li>
			</ul>
			<p>
				Currently <span class="title">Names on Nodes</span> is in development.
				It is not yet known when it will be launched.
				Progress can be tracked at Mike Keesey's blog, <a href="http://3lbmonkeybrain.blogspot.com/search/label/Names%20on%20Nodes" class="title">A Three-Pound Monkey Brain</a>.
			</p>
			<h2>Documentation</h2>
			<h3><span class="langname">MathML</span> Definitions</h3>
			<p>
				<span class="title">Names on Nodes</span> uses <a href="http://www.w3.org/TR/MathML2/" class="langname">MathML 2.0</a> to model nomenclatural definitions.
				To accomplish this, it relies on certain mathematical entities related to phylogeny and taxonomy.
				These are defined and discussed in the <a href="./ns/math/2009/index.html"><span class="title"><span class="langname">MathML</span> Definitions</span> document</a>.
				(Note that this document is currently in draft form, with some incomplete sections.)
			</p>
			<h3>Entities</h3>
			<p>
				Although <span class="title">Names on Nodes</span> will primarily store information in a database, it will also be capable of reading entity information from <span class="langname">XML</span> files.
				The <span class="langname">XML</span> format is laid out in the <a href="./ns/entities/2009/index.html"><span class="title">Entity Definitions</span> document</a>.
			</p>
			<h2>Open Source Code</h2>
			<p>
				The <span class="title">Names on Nodes</span> source code (primarily Java, ActionScript, and MXML) has been moved to <span class="title">Google Code</span>.
				It is not currently in clean condition, but if you would like to check it out you may do so at the following URL: <a href="http://code.google.com/p/namesonnodes/"><code>http://code.google.com/p/namesonnodes</code></a>
			</p>
			<h2>Demo Tools</h2>
			<p>
				Until <span class="title">Names on Nodes</span> is complete, a series of small applications will be released online in order to showcase some of the functionality.
				These present an opportunity to test certain components before the final application is complete.
			</p>
			<h3><span class="title"><span class="langname">Nexus</span> Viewer</span></h3>
			<p>
				<span class="title"><span class="langname">Nexus</span> Viewer</span> opens <span class="langname">Nexus</span> files and displays the trees in them combined into a single phylogenetic network.
				(Note that this only works properly for <span class="langname">Nexus</span> files with rooted trees.
				For files without rooted trees, it will simply display a series of operational taxonomic units.)
				<a href="./nexusdemo">Click here.</a>
			</p>
			<h3><span class="title">Text Tree Maker</span></h3>
			<p>
				<span class="title">Text Tree Maker</span> converts Newick tree strings into readable text cladograms.
				<a href="./texttree">Click here.</a>
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